| Title: “Differential Expression Identification” |
| Purpose: “ASPIS omics Steatosis case study” |
| Input.data: “NormData_TG_Gates_Hum_invitro_ENS.txt” |
| Author: “Marcha Verheijen (ONTOX)” |
| Date: ‘2024-01-11’ |
for Microarray technology was used. (Publication: “R-ODAF: Omics data analysis framework for regulatory application”, 2022, Regulatory Toxicology and Pharmacology.) This pipeline can be found at https://github.com/R-ODAF/Main and was based on:
a tool for statistical analysis of Affymetrix expression data. Copyright 2010-2014 BiGCaT Bioinformatics
| Array | Name | CompoundClass | Group | Group_Dose | SteatosisPotential | Group_Time | CompoundName | DoseGroup | Treatment | TimeDose | TimeDose_low | TimeDose_middle | TimeDose_high | TimeDose2 | TimeDose_middlehigh | DoseValue | DoseUnit | Time | TimeUnit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 003016027024.CEL | TG_hum_vit_Ami_ctl_2h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | amiodarone_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016027025.CEL | TG_hum_vit_Ami_ctl_2h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | amiodarone_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016028006.CEL | TG_hum_vit_Ami_ctl_8h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | amiodarone_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016028007.CEL | TG_hum_vit_Ami_ctl_8h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | amiodarone_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016028014.CEL | TG_hum_vit_Ami_ctl_24h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | amiodarone_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016028015.CEL | TG_hum_vit_Ami_ctl_24h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | amiodarone_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016027026.CEL | TG_hum_vit_Ami_280nm_2h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | amiodarone_Low | Low | amiodarone | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 0.28 | micromolar | 2 | hour | |||
| 003016028001.CEL | TG_hum_vit_Ami_280nm_2h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | amiodarone_Low | Low | amiodarone | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 0.28 | micromolar | 2 | hour | |||
| 003016028008.CEL | TG_hum_vit_Ami_280nm_8h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | amiodarone_Low | Low | amiodarone | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 0.28 | micromolar | 8 | hour | |||
| 003016028009.CEL | TG_hum_vit_Ami_280nm_8h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | amiodarone_Low | Low | amiodarone | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 0.28 | micromolar | 8 | hour | |||
| 003016028016.CEL | TG_hum_vit_Ami_280nm_24h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | amiodarone_Low | Low | amiodarone | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 0.28 | micromolar | 24 | hour | |||
| 003016028017.CEL | TG_hum_vit_Ami_280nm_24h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | amiodarone_Low | Low | amiodarone | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 0.28 | micromolar | 24 | hour | |||
| 003016028002.CEL | TG_hum_vit_Ami_1400nm_2h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | amiodarone_Middle | Middle | amiodarone | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1.40 | micromolar | 2 | hour | ||
| 003016028003.CEL | TG_hum_vit_Ami_1400nm_2h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | amiodarone_Middle | Middle | amiodarone | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1.40 | micromolar | 2 | hour | ||
| 003016028010.CEL | TG_hum_vit_Ami_1400nm_8h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | amiodarone_Middle | Middle | amiodarone | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1.40 | micromolar | 8 | hour | ||
| 003016028011.CEL | TG_hum_vit_Ami_1400nm_8h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | amiodarone_Middle | Middle | amiodarone | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1.40 | micromolar | 8 | hour | ||
| 003016028018.CEL | TG_hum_vit_Ami_1400nm_24h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | amiodarone_Middle | Middle | amiodarone | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1.40 | micromolar | 24 | hour | ||
| 003016028019.CEL | TG_hum_vit_Ami_1400nm_24h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | amiodarone_Middle | Middle | amiodarone | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1.40 | micromolar | 24 | hour | ||
| 003016028004.CEL | TG_hum_vit_Ami_7um_2h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | amiodarone_High | High | amiodarone | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 7.00 | micromolar | 2 | hour | ||
| 003016028005.CEL | TG_hum_vit_Ami_7um_2h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | amiodarone_High | High | amiodarone | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 7.00 | micromolar | 2 | hour | ||
| 003016028012.CEL | TG_hum_vit_Ami_7um_8h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | amiodarone_High | High | amiodarone | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 7.00 | micromolar | 8 | hour | ||
| 003016028013.CEL | TG_hum_vit_Ami_7um_8h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | amiodarone_High | High | amiodarone | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 7.00 | micromolar | 8 | hour | ||
| 003016028020.CEL | TG_hum_vit_Ami_7um_24h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | amiodarone_High | High | amiodarone | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 7.00 | micromolar | 24 | hour | ||
| 003016028021.CEL | TG_hum_vit_Ami_7um_24h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | amiodarone_High | High | amiodarone | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 7.00 | micromolar | 24 | hour | ||
| 003016018004.CEL | TG_hum_vit_Ctc_ctl_2h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | carbon tetrachloride_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016018005.CEL | TG_hum_vit_Ctc_ctl_2h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | carbon tetrachloride_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016018012.CEL | TG_hum_vit_Ctc_ctl_8h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | carbon tetrachloride_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016018013.CEL | TG_hum_vit_Ctc_ctl_8h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | carbon tetrachloride_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016018020.CEL | TG_hum_vit_Ctc_ctl_24h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | carbon tetrachloride_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016018021.CEL | TG_hum_vit_Ctc_ctl_24h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | carbon tetrachloride_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016018006.CEL | TG_hum_vit_Ctc_300um_2h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 300.00 | micromolar | 2 | hour | |||
| 003016018007.CEL | TG_hum_vit_Ctc_300um_2h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 300.00 | micromolar | 2 | hour | |||
| 003016018014.CEL | TG_hum_vit_Ctc_300um_8h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 300.00 | micromolar | 8 | hour | |||
| 003016018015.CEL | TG_hum_vit_Ctc_300um_8h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 300.00 | micromolar | 8 | hour | |||
| 003016018022.CEL | TG_hum_vit_Ctc_300um_24h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 300.00 | micromolar | 24 | hour | |||
| 003016018023.CEL | TG_hum_vit_Ctc_300um_24h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | carbon tetrachloride_Low | Low | carbon tetrachloride | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 300.00 | micromolar | 24 | hour | |||
| 003016018008.CEL | TG_hum_vit_Ctc_1500um_2h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1500.00 | micromolar | 2 | hour | ||
| 003016018009.CEL | TG_hum_vit_Ctc_1500um_2h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1500.00 | micromolar | 2 | hour | ||
| 003016018016.CEL | TG_hum_vit_Ctc_1500um_8h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1500.00 | micromolar | 8 | hour | ||
| 003016018017.CEL | TG_hum_vit_Ctc_1500um_8h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1500.00 | micromolar | 8 | hour | ||
| 003016018024.CEL | TG_hum_vit_Ctc_1500um_24h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1500.00 | micromolar | 24 | hour | ||
| 003016018025.CEL | TG_hum_vit_Ctc_1500um_24h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | carbon tetrachloride_Middle | Middle | carbon tetrachloride | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1500.00 | micromolar | 24 | hour | ||
| 003016018010.CEL | TG_hum_vit_Ctc_7500um_2h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 7500.00 | micromolar | 2 | hour | ||
| 003016018011.CEL | TG_hum_vit_Ctc_7500um_2h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 7500.00 | micromolar | 2 | hour | ||
| 003016018018.CEL | TG_hum_vit_Ctc_7500um_8h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 7500.00 | micromolar | 8 | hour | ||
| 003016018019.CEL | TG_hum_vit_Ctc_7500um_8h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 7500.00 | micromolar | 8 | hour | ||
| 003016018026.CEL | TG_hum_vit_Ctc_7500um_24h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 7500.00 | micromolar | 24 | hour | ||
| 003016018027.CEL | TG_hum_vit_Ctc_7500um_24h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | carbon tetrachloride_High | High | carbon tetrachloride | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 7500.00 | micromolar | 24 | hour | ||
| 003016075024.CEL | TG_hum_vit_Col_ctl_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_8h | colchicine_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016075025.CEL | TG_hum_vit_Col_ctl_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_8h | colchicine_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016075030.CEL | TG_hum_vit_Col_ctl_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_24h | colchicine_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016076030.CEL | TG_hum_vit_Col_ctl_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_24h | colchicine_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016075026.CEL | TG_hum_vit_Col_800um_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_8h | colchicine_Middle | Middle | colchicine | Non_steatotic_8h_Middle | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 800.00 | micromolar | 8 | hour | ||
| 003016075027.CEL | TG_hum_vit_Col_800um_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_8h | colchicine_Middle | Middle | colchicine | Non_steatotic_8h_Middle | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 800.00 | micromolar | 8 | hour | ||
| 003016076002.CEL | TG_hum_vit_Col_800um_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_24h | colchicine_Middle | Middle | colchicine | Non_steatotic_24h_Middle | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 800.00 | micromolar | 24 | hour | ||
| 003016076003.CEL | TG_hum_vit_Col_800um_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_24h | colchicine_Middle | Middle | colchicine | Non_steatotic_24h_Middle | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 800.00 | micromolar | 24 | hour | ||
| 003016075028.CEL | TG_hum_vit_Col_4000um_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_8h | colchicine_High | High | colchicine | Non_steatotic_8h_High | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 4000.00 | micromolar | 8 | hour | ||
| 003016075029.CEL | TG_hum_vit_Col_4000um_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_8h | colchicine_High | High | colchicine | Non_steatotic_8h_High | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 4000.00 | micromolar | 8 | hour | ||
| 003016076004.CEL | TG_hum_vit_Col_4000um_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_24h | colchicine_High | High | colchicine | Non_steatotic_24h_High | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 4000.00 | micromolar | 24 | hour | ||
| 003016076005.CEL | TG_hum_vit_Col_4000um_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_24h | colchicine_High | High | colchicine | Non_steatotic_24h_High | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 4000.00 | micromolar | 24 | hour | ||
| 003016065008.CEL | TG_hum_vit_Imi_ctl_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_8h | imipramine_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016065009.CEL | TG_hum_vit_Imi_ctl_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_8h | imipramine_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016065014.CEL | TG_hum_vit_Imi_ctl_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_24h | imipramine_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016065015.CEL | TG_hum_vit_Imi_ctl_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Control | none | Non_steatotic_24h | imipramine_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016065010.CEL | TG_hum_vit_Imi_3um_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_8h | imipramine_Middle | Middle | imipramine | Non_steatotic_8h_Middle | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 3.00 | micromolar | 8 | hour | ||
| 003016065011.CEL | TG_hum_vit_Imi_3um_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_8h | imipramine_Middle | Middle | imipramine | Non_steatotic_8h_Middle | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 3.00 | micromolar | 8 | hour | ||
| 003016065016.CEL | TG_hum_vit_Imi_3um_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_24h | imipramine_Middle | Middle | imipramine | Non_steatotic_24h_Middle | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 3.00 | micromolar | 24 | hour | ||
| 003016065017.CEL | TG_hum_vit_Imi_3um_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_Middle | none | Non_steatotic_24h | imipramine_Middle | Middle | imipramine | Non_steatotic_24h_Middle | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 3.00 | micromolar | 24 | hour | ||
| 003016065012.CEL | TG_hum_vit_Imi_15um_8h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_8h | imipramine_High | High | imipramine | Non_steatotic_8h_High | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 15.00 | micromolar | 8 | hour | ||
| 003016065013.CEL | TG_hum_vit_Imi_15um_8h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_8h | imipramine_High | High | imipramine | Non_steatotic_8h_High | Non_steatotic_8h_Control | Non_steatotic_8h_MiddleHigh | Non_steatotic_8h_Control | 15.00 | micromolar | 8 | hour | ||
| 003016065018.CEL | TG_hum_vit_Imi_15um_24h_1 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_24h | imipramine_High | High | imipramine | Non_steatotic_24h_High | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 15.00 | micromolar | 24 | hour | ||
| 003016065019.CEL | TG_hum_vit_Imi_15um_24h_2 | Non_Steatotic | Non_steatotic | Non_Steatotic_High | none | Non_steatotic_24h | imipramine_High | High | imipramine | Non_steatotic_24h_High | Non_steatotic_24h_Control | Non_steatotic_24h_MiddleHigh | Non_steatotic_24h_Control | 15.00 | micromolar | 24 | hour | ||
| 003016060014.CEL | TG_hum_vit_Tam_ctl_8h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | tamoxifen_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016060015.CEL | TG_hum_vit_Tam_ctl_8h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | tamoxifen_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016060020.CEL | TG_hum_vit_Tam_ctl_24h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | tamoxifen_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016060021.CEL | TG_hum_vit_Tam_ctl_24h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | tamoxifen_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016060016.CEL | TG_hum_vit_Tam_5um_8h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | tamoxifen_Middle | Middle | tamoxifen | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 5.00 | micromolar | 8 | hour | ||
| 003016060017.CEL | TG_hum_vit_Tam_5um_8h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | tamoxifen_Middle | Middle | tamoxifen | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 5.00 | micromolar | 8 | hour | ||
| 003016060022.CEL | TG_hum_vit_Tam_5um_24h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | tamoxifen_Middle | Middle | tamoxifen | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 5.00 | micromolar | 24 | hour | ||
| 003016060023.CEL | TG_hum_vit_Tam_5um_24h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | tamoxifen_Middle | Middle | tamoxifen | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 5.00 | micromolar | 24 | hour | ||
| 003016060018.CEL | TG_hum_vit_Tam_25um_8h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | tamoxifen_High | High | tamoxifen | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 25.00 | micromolar | 8 | hour | ||
| 003016060019.CEL | TG_hum_vit_Tam_25um_8h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | tamoxifen_High | High | tamoxifen | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 25.00 | micromolar | 8 | hour | ||
| 003016060024.CEL | TG_hum_vit_Tam_25um_24h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | tamoxifen_High | High | tamoxifen | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 25.00 | micromolar | 24 | hour | ||
| 003016060025.CEL | TG_hum_vit_Tam_25um_24h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | tamoxifen_High | High | tamoxifen | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 25.00 | micromolar | 24 | hour | ||
| 003016037018.CEL | TG_hum_vit_Vpa_ctl_2h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | valproic acid_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016037019.CEL | TG_hum_vit_Vpa_ctl_2h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_2h | valproic acid_Control | Control | none | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | Non_steatotic_2h_Control | NA | 2 | hour | |
| 003016037026.CEL | TG_hum_vit_Vpa_ctl_8h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | valproic acid_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016037027.CEL | TG_hum_vit_Vpa_ctl_8h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_8h | valproic acid_Control | Control | none | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | Non_steatotic_8h_Control | NA | 8 | hour | |
| 003016038004.CEL | TG_hum_vit_Vpa_ctl_24h_1 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | valproic acid_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016038005.CEL | TG_hum_vit_Vpa_ctl_24h_2 | Steatotic | Non_steatotic | Steatotic_Control | none | Non_steatotic_24h | valproic acid_Control | Control | none | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | Non_steatotic_24h_Control | NA | 24 | hour | |
| 003016037020.CEL | TG_hum_vit_Vpa_200um_2h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | valproic acid_Low | Low | valproic acid | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 200.00 | micromolar | 2 | hour | |||
| 003016037021.CEL | TG_hum_vit_Vpa_200um_2h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_2h | valproic acid_Low | Low | valproic acid | Steatotic_2h_Low | Steatotic_2h_Low | Steatotic_2h_Low | 200.00 | micromolar | 2 | hour | |||
| 003016037028.CEL | TG_hum_vit_Vpa_200um_8h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | valproic acid_Low | Low | valproic acid | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 200.00 | micromolar | 8 | hour | |||
| 003016037029.CEL | TG_hum_vit_Vpa_200um_8h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_8h | valproic acid_Low | Low | valproic acid | Steatotic_8h_Low | Steatotic_8h_Low | Steatotic_8h_Low | 200.00 | micromolar | 8 | hour | |||
| 003016038006.CEL | TG_hum_vit_Vpa_200um_24h_1 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | valproic acid_Low | Low | valproic acid | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 200.00 | micromolar | 24 | hour | |||
| 003016038007.CEL | TG_hum_vit_Vpa_200um_24h_2 | Steatotic | Steatotic | Steatotic_Low | low | Steatotic_24h | valproic acid_Low | Low | valproic acid | Steatotic_24h_Low | Steatotic_24h_Low | Steatotic_24h_Low | 200.00 | micromolar | 24 | hour | |||
| 003016037022.CEL | TG_hum_vit_Vpa_1000um_2h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | valproic acid_Middle | Middle | valproic acid | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1000.00 | micromolar | 2 | hour | ||
| 003016037023.CEL | TG_hum_vit_Vpa_1000um_2h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_2h | valproic acid_Middle | Middle | valproic acid | Steatotic_2h_Middle | Steatotic_2h_Middle | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 1000.00 | micromolar | 2 | hour | ||
| 003016037030.CEL | TG_hum_vit_Vpa_1000um_8h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | valproic acid_Middle | Middle | valproic acid | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1000.00 | micromolar | 8 | hour | ||
| 003016038001.CEL | TG_hum_vit_Vpa_1000um_8h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_8h | valproic acid_Middle | Middle | valproic acid | Steatotic_8h_Middle | Steatotic_8h_Middle | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 1000.00 | micromolar | 8 | hour | ||
| 003016038008.CEL | TG_hum_vit_Vpa_1000um_24h_1 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | valproic acid_Middle | Middle | valproic acid | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1000.00 | micromolar | 24 | hour | ||
| 003016038009.CEL | TG_hum_vit_Vpa_1000um_24h_2 | Steatotic | Steatotic | Steatotic_Middle | middle | Steatotic_24h | valproic acid_Middle | Middle | valproic acid | Steatotic_24h_Middle | Steatotic_24h_Middle | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 1000.00 | micromolar | 24 | hour | ||
| 003016037024.CEL | TG_hum_vit_Vpa_5000um_2h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | valproic acid_High | High | valproic acid | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 5000.00 | micromolar | 2 | hour | ||
| 003016037025.CEL | TG_hum_vit_Vpa_5000um_2h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_2h | valproic acid_High | High | valproic acid | Steatotic_2h_High | Steatotic_2h_High | Steatotic_2h_MiddleHigh | Steatotic_2h_MiddleHigh | 5000.00 | micromolar | 2 | hour | ||
| 003016038002.CEL | TG_hum_vit_Vpa_5000um_8h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | valproic acid_High | High | valproic acid | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 5000.00 | micromolar | 8 | hour | ||
| 003016038003.CEL | TG_hum_vit_Vpa_5000um_8h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_8h | valproic acid_High | High | valproic acid | Steatotic_8h_High | Steatotic_8h_High | Steatotic_8h_MiddleHigh | Steatotic_8h_MiddleHigh | 5000.00 | micromolar | 8 | hour | ||
| 003016038010.CEL | TG_hum_vit_Vpa_5000um_24h_1 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | valproic acid_High | High | valproic acid | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 5000.00 | micromolar | 24 | hour | ||
| 003016038011.CEL | TG_hum_vit_Vpa_5000um_24h_2 | Steatotic | Steatotic | Steatotic_High | high | Steatotic_24h | valproic acid_High | High | valproic acid | Steatotic_24h_High | Steatotic_24h_High | Steatotic_24h_MiddleHigh | Steatotic_24h_MiddleHigh | 5000.00 | micromolar | 24 | hour |
# Set input parameters
cutOffAdj.P.Val <- 0.05
cutOfflogFC <- 0
cutOffAveExpr <- 6
cutOffPval <- 0.05 #used if Adj.P.Val removes all
# Groups to compare
Description_column<-"Group"
InterestGroup<- "Steatotic"
Controls<-"Non_steatotic"
# remove unused metadata
descriptionTable2<-descriptionTable[,c("Array", "Name", Description_column)]
write.table(descriptionTable2, paste0(descriptionFile, "_sub.txt"), row.names=FALSE, quote=FALSE, sep="\t")
# remove unused samples
descriptionTable2<- descriptionTable2[c(grep(InterestGroup,descriptionTable2[,Description_column]), grep(Controls,descriptionTable2[,Description_column])),]
colnames(descriptionTable2)<-c("Array", "Name", "experimentFactor")
normDataTable<-normDataTable[,c(descriptionTable2$Name)]
| Var1 | Freq |
|---|---|
| Non_steatotic | 46 |
| Steatotic | 62 |
## --[[ Saving table for contrast Steatoticx1+Non_steatoticx-1 ]]--
## [1] "p-value histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt P.Value_hist.png ]]--
## [1] "adapted fold change histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt FC_hist.png ]]--
## [1] "Creating table based on the cut-offs"
## [1] "Applying cutOffAveExpr (6) removed 11642 genes. 8272 genes remain."
## [1] "Additionally, applying cutOfflogFC (0) removed 0 genes. 8272 genes remain."
## [1] "Additionally, applying cutOffAdj.P.Val (0.05) removed 5125 genes. 3147 genes remain."
## --[[ Saving table Steatoticx1+Non_steatoticx-1_chosen_cutOff.txt ]]--
## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=Dutch_Netherlands.utf8 LC_CTYPE=Dutch_Netherlands.utf8
## [3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C
## [5] LC_TIME=Dutch_Netherlands.utf8
##
## time zone: Europe/Amsterdam
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] gdata_3.0.0 limma_3.56.2 umap_0.2.10.0 plotly_4.10.3 ggplot2_3.4.4
## [6] DT_0.30 knitr_1.45
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.7 utf8_1.2.4 generics_0.1.3 tidyr_1.3.0
## [5] gtools_3.9.4 lattice_0.21-8 digest_0.6.33 magrittr_2.0.3
## [9] evaluate_0.23 grid_4.3.1 fastmap_1.1.1 jsonlite_1.8.7
## [13] Matrix_1.5-4.1 RSpectra_0.16-1 httr_1.4.7 purrr_1.0.2
## [17] fansi_1.0.5 crosstalk_1.2.0 viridisLite_0.4.2 scales_1.2.1
## [21] lazyeval_0.2.2 jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1
## [25] ellipsis_0.3.2 munsell_0.5.0 yaml_2.3.7 withr_2.5.2
## [29] cachem_1.0.8 tools_4.3.1 dplyr_1.1.3 colorspace_2.1-0
## [33] reticulate_1.34.0 vctrs_0.6.4 R6_2.5.1 png_0.1-8
## [37] lifecycle_1.0.4 htmlwidgets_1.6.2 pkgconfig_2.0.3 pillar_1.9.0
## [41] bslib_0.5.1 gtable_0.3.4 data.table_1.14.8 glue_1.6.2
## [45] Rcpp_1.0.11 xfun_0.39 tibble_3.2.1 tidyselect_1.2.0
## [49] highr_0.10 farver_2.1.1 htmltools_0.5.5 rmarkdown_2.25
## [53] compiler_4.3.1 askpass_1.2.0 openssl_2.1.1
End of Report